So after some testing, I think I may have found the root cause of the bug where a placed or built ship dances around like an epileptic kid at a rave, despite being off. Its the RAMPS! There are many designs out there with retractable ramps that go down to ground level, or possible below. When the ramp is retracted, you would think it has the collision box of the retracted size, right? Wrong. You can test this yourself, take an otherwise stable ship, put a ramp on it that would open down into the ground, but would be above ground level when retracted. Retract said ramp. And don’t forget to “turn on your lights, so it turns it into a disco ball”. Voila. Magical dancing ship.
I found one solution to a ship that is actively dancing is to take a block and extend a line downward into the ground. This pops the ship up once, yes, but then it lands on the normal collision box of the block, not on the ramp.
Hope this helps, Let me know if it does, or if you find a counter example.